Mapion 
Current maps of Japan which can be generated from address, prefecture, landmark names, zip code, train station or street name. It can also provide distance measurements and map routes which combine different modes of transportation (eg: train and foot).

Yahoo Maps Japan
Current maps of all Japanese regions and prefectures. When zoomed closely there are clickable restaurants and medical clinics, in addition to other points of interest.

Google Map
Current maps and satellite images of Japan.  Test your knowledge of Tokyo geography.

Tokyo GIS Plaza
Useful GIS data for Japan. 

Interactive Geological Hazard Map of East and Southeast Asia
Provides information on volcanoes, earthquakes, tsunamis and landslides in Japan, China, South Korea, Thailand, Cambodia, Vietnam, Indonesia, Malaysia and the Philippines.